Starting phenix.real_space_refine
on Wed Sep 17 13:03:59 2025 by dcliebschner
===============================================================================

Processing files:
-------------------------------------------------------------------------------

  Found model, /net/cci-nas-00/data/ceres_data/9gsj_51550/09_2025/9gsj_51550.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9gsj_51550/09_2025/9gsj_51550.map

Processing PHIL parameters:
-------------------------------------------------------------------------------

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.6
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9gsj_51550/09_2025/9gsj_51550.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9gsj_51550/09_2025/9gsj_51550.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9gsj_51550/09_2025/9gsj_51550.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9gsj_51550/09_2025/9gsj_51550.map"
  }
  resolution = 3.6
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


Starting job
===============================================================================
-------------------------------------------------------------------------------
Citation:
*********
Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams
PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography.
Acta Cryst. D74:531-544.

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.002 sd=   0.025
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      36      5.16       5
     C    5704      2.51       5
     N    1480      2.21       5
     O    1650      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 5 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 8870
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 4401
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 572, 4401
          Classifications: {'peptide': 572}
          Link IDs: {'PTRANS': 17, 'TRANS': 554}
    Chain: "B"
      Number of atoms: 4401
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 572, 4401
          Classifications: {'peptide': 572}
          Link IDs: {'PTRANS': 17, 'TRANS': 554}
    Chain: "A"
      Number of atoms: 34
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 34
          Unusual residues: {'HT1': 1}
          Classifications: {'undetermined': 1}
    Chain: "B"
      Number of atoms: 34
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 34
          Unusual residues: {'HT1': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 2.38, per 1000 atoms: 0.27
  Number of scatterers: 8870
  At special positions: 0
  Unit cell: (76.349, 113.265, 132.562, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      36     16.00
     O    1650      8.00
     N    1480      7.00
     C    5704      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.87
  Conformation dependent library (CDL) restraints added in 236.2 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  2280 Ramachandran restraints generated.
    1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2104

  Finding SS restraints...
    Secondary structure from input PDB file:
      43 helices and 4 sheets defined
      69.5% alpha, 5.2% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.30
  Creating SS restraints...
    Processing helix  chain 'A' and resid 12 through 22
      removed outlier: 3.743A  pdb=" N   THR A  22 " --> pdb=" O   LEU A  18 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 25 through 44
    Processing helix  chain 'A' and resid 45 through 57
    Processing helix  chain 'A' and resid 59 through 110
      removed outlier: 3.803A  pdb=" N   SER A  63 " --> pdb=" O   MET A  59 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 111 through 118
      removed outlier: 3.922A  pdb=" N   PHE A 115 " --> pdb=" O   PRO A 111 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 120 through 140
      removed outlier: 4.221A  pdb=" N   VAL A 124 " --> pdb=" O   SER A 120 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 140 through 163
    Processing helix  chain 'A' and resid 163 through 174
      removed outlier: 4.468A  pdb=" N   THR A 167 " --> pdb=" O   ASN A 163 " (cutoff:3.500A)
      removed outlier: 3.869A  pdb=" N   LEU A 168 " --> pdb=" O   TRP A 164 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 177 through 210
      Proline residue:  A 183  - end of helix
    Processing helix  chain 'A' and resid 212 through 219
    Processing helix  chain 'A' and resid 221 through 249
    Processing helix  chain 'A' and resid 250 through 275
      removed outlier: 3.673A  pdb=" N   SER A 255 " --> pdb=" O   GLY A 251 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 281 through 321
      removed outlier: 4.242A  pdb=" N   MET A 295 " --> pdb=" O   PHE A 291 " (cutoff:3.500A)
      Proline residue:  A 296  - end of helix
      removed outlier: 4.176A  pdb=" N   GLY A 312 " --> pdb=" O   GLN A 308 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 379 through 388
    Processing helix  chain 'A' and resid 409 through 416
      removed outlier: 3.589A  pdb=" N   HIS A 416 " --> pdb=" O   SER A 412 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 430 through 436
    Processing helix  chain 'A' and resid 446 through 455
      removed outlier: 4.369A  pdb=" N   LYS A 450 " --> pdb=" O   ALA A 446 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 480 through 496
      removed outlier: 3.614A  pdb=" N   ARG A 484 " --> pdb=" O   SER A 480 " (cutoff:3.500A)
      removed outlier: 3.617A  pdb=" N   ARG A 486 " --> pdb=" O   GLY A 482 " (cutoff:3.500A)
      removed outlier: 3.955A  pdb=" N   ASN A 496 " --> pdb=" O   ALA A 492 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 509 through 525
      removed outlier: 4.192A  pdb=" N   SER A 513 " --> pdb=" O   LEU A 509 " (cutoff:3.500A)
      removed outlier: 3.870A  pdb=" N   SER A 516 " --> pdb=" O   GLN A 512 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 526 through 528
      No H-bonds generated for 'chain 'A' and resid 526 through 528'
    Processing helix  chain 'A' and resid 560 through 568
      removed outlier: 4.118A  pdb=" N   SER A 566 " --> pdb=" O   GLU A 562 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 570 through 581
    Processing helix  chain 'B' and resid 12 through 21
    Processing helix  chain 'B' and resid 25 through 57
      removed outlier: 3.799A  pdb=" N   LEU B  29 " --> pdb=" O   SER B  25 " (cutoff:3.500A)
      Proline residue:  B  47  - end of helix
    Processing helix  chain 'B' and resid 59 through 110
      removed outlier: 3.822A  pdb=" N   SER B  63 " --> pdb=" O   MET B  59 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 111 through 119
      removed outlier: 3.706A  pdb=" N   PHE B 115 " --> pdb=" O   PRO B 111 " (cutoff:3.500A)
      removed outlier: 3.640A  pdb=" N   THR B 117 " --> pdb=" O   SER B 113 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 120 through 140
      removed outlier: 4.176A  pdb=" N   VAL B 124 " --> pdb=" O   SER B 120 " (cutoff:3.500A)
      removed outlier: 5.068A  pdb=" N   ASP B 130 " --> pdb=" O   ARG B 126 " (cutoff:3.500A)
      removed outlier: 4.236A  pdb=" N   THR B 131 " --> pdb=" O   VAL B 127 " (cutoff:3.500A)
      removed outlier: 3.723A  pdb=" N   MET B 132 " --> pdb=" O   THR B 128 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 140 through 163
    Processing helix  chain 'B' and resid 163 through 174
      removed outlier: 4.172A  pdb=" N   THR B 167 " --> pdb=" O   ASN B 163 " (cutoff:3.500A)
      removed outlier: 3.605A  pdb=" N   LEU B 168 " --> pdb=" O   TRP B 164 " (cutoff:3.500A)
      removed outlier: 3.823A  pdb=" N   VAL B 170 " --> pdb=" O   LEU B 166 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 177 through 210
      Proline residue:  B 183  - end of helix
    Processing helix  chain 'B' and resid 212 through 220
    Processing helix  chain 'B' and resid 221 through 249
    Processing helix  chain 'B' and resid 250 through 276
      removed outlier: 3.545A  pdb=" N   GLY B 276 " --> pdb=" O   GLN B 272 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 282 through 323
      removed outlier: 3.750A  pdb=" N   MET B 295 " --> pdb=" O   PHE B 291 " (cutoff:3.500A)
      Proline residue:  B 296  - end of helix
      removed outlier: 3.959A  pdb=" N   GLN B 299 " --> pdb=" O   MET B 295 " (cutoff:3.500A)
      removed outlier: 4.080A  pdb=" N   GLU B 315 " --> pdb=" O   ILE B 311 " (cutoff:3.500A)
      removed outlier: 3.846A  pdb=" N   ARG B 316 " --> pdb=" O   GLY B 312 " (cutoff:3.500A)
      removed outlier: 3.773A  pdb=" N   GLU B 323 " --> pdb=" O   GLU B 319 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 379 through 388
      removed outlier: 3.667A  pdb=" N   GLU B 388 " --> pdb=" O   PHE B 384 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 409 through 416
      removed outlier: 3.510A  pdb=" N   HIS B 416 " --> pdb=" O   SER B 412 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 430 through 437
      removed outlier: 3.593A  pdb=" N   ASN B 434 " --> pdb=" O   THR B 430 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 447 through 455
    Processing helix  chain 'B' and resid 480 through 496
      removed outlier: 3.930A  pdb=" N   ASN B 496 " --> pdb=" O   ALA B 492 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 509 through 526
      removed outlier: 3.878A  pdb=" N   SER B 513 " --> pdb=" O   LEU B 509 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 536 through 542
    Processing helix  chain 'B' and resid 559 through 571
    Processing helix  chain 'B' and resid 571 through 581
      removed outlier: 4.347A  pdb=" N   GLU B 575 " --> pdb=" O   ARG B 571 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 360 through 364
      removed outlier: 7.451A  pdb=" N   ALA A 362 " --> pdb=" O   ASP A 344 " (cutoff:3.500A)
      removed outlier: 5.168A  pdb=" N   ASP A 344 " --> pdb=" O   ALA A 362 " (cutoff:3.500A)
      removed outlier: 7.163A  pdb=" N   ILE A 364 " --> pdb=" O   GLN A 342 " (cutoff:3.500A)
      removed outlier: 5.256A  pdb=" N   GLN A 342 " --> pdb=" O   ILE A 364 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 417 through 420
      removed outlier: 6.057A  pdb=" N   GLY A 418 " --> pdb=" O   MET A 501 " (cutoff:3.500A)
      removed outlier: 6.232A  pdb=" N   THR A 370 " --> pdb=" O   VAL A 532 " (cutoff:3.500A)
      removed outlier: 6.378A  pdb=" N   VAL A 369 " --> pdb=" O   GLN A 545 " (cutoff:3.500A)
      removed outlier: 7.825A  pdb=" N   LEU A 547 " --> pdb=" O   VAL A 369 " (cutoff:3.500A)
      removed outlier: 5.835A  pdb=" N   ALA A 371 " --> pdb=" O   LEU A 547 " (cutoff:3.500A)
      removed outlier: 7.332A  pdb=" N   VAL A 549 " --> pdb=" O   ALA A 371 " (cutoff:3.500A)
      removed outlier: 6.376A  pdb=" N   VAL A 373 " --> pdb=" O   VAL A 549 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 360 through 364
      removed outlier: 7.769A  pdb=" N   ALA B 362 " --> pdb=" O   ASP B 344 " (cutoff:3.500A)
      removed outlier: 5.500A  pdb=" N   ASP B 344 " --> pdb=" O   ALA B 362 " (cutoff:3.500A)
      removed outlier: 6.897A  pdb=" N   ILE B 364 " --> pdb=" O   GLN B 342 " (cutoff:3.500A)
      removed outlier: 4.745A  pdb=" N   GLN B 342 " --> pdb=" O   ILE B 364 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 417 through 420
      removed outlier: 6.217A  pdb=" N   GLY B 418 " --> pdb=" O   MET B 501 " (cutoff:3.500A)
      removed outlier: 6.070A  pdb=" N   THR B 370 " --> pdb=" O   VAL B 532 " (cutoff:3.500A)
      removed outlier: 6.333A  pdb=" N   VAL B 369 " --> pdb=" O   GLN B 545 " (cutoff:3.500A)
      removed outlier: 7.877A  pdb=" N   LEU B 547 " --> pdb=" O   VAL B 369 " (cutoff:3.500A)
      removed outlier: 6.312A  pdb=" N   ALA B 371 " --> pdb=" O   LEU B 547 " (cutoff:3.500A)
      removed outlier: 7.525A  pdb=" N   VAL B 549 " --> pdb=" O   ALA B 371 " (cutoff:3.500A)
      removed outlier: 6.448A  pdb=" N   VAL B 373 " --> pdb=" O   VAL B 549 " (cutoff:3.500A)

    591 hydrogen bonds defined for protein.
    1755 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.40

  Time building geometry restraints manager: 1.06 seconds

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.

  Histogram of bond lengths:
        1.23 -     1.34: 2861
        1.34 -     1.46: 1922
        1.46 -     1.58: 4161
        1.58 -     1.70: 0
        1.70 -     1.82: 70
  Bond restraints: 9014
  Sorted by residual:
  bond pdb=" N   MET A 525 "
       pdb=" CA  MET A 525 "
    ideal  model  delta    sigma   weight residual
    1.456  1.492 -0.036 1.18e-02 7.18e+03 9.32e+00
  bond pdb=" N   GLU B 277 "
       pdb=" CA  GLU B 277 "
    ideal  model  delta    sigma   weight residual
    1.456  1.475 -0.020 1.25e-02 6.40e+03 2.52e+00
  bond pdb=" N   THR B 279 "
       pdb=" CA  THR B 279 "
    ideal  model  delta    sigma   weight residual
    1.457  1.477 -0.020 1.29e-02 6.01e+03 2.29e+00
  bond pdb=" N   LEU B 278 "
       pdb=" CA  LEU B 278 "
    ideal  model  delta    sigma   weight residual
    1.457  1.476 -0.019 1.30e-02 5.92e+03 2.08e+00
  bond pdb=" C   VAL A 174 "
       pdb=" N   PRO A 175 "
    ideal  model  delta    sigma   weight residual
    1.334  1.364 -0.030 2.34e-02 1.83e+03 1.60e+00
  ... (remaining 9009 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.07: 11941
        2.07 -     4.13: 208
        4.13 -     6.20: 37
        6.20 -     8.26: 12
        8.26 -    10.33: 8
  Bond angle restraints: 12206
  Sorted by residual:
  angle pdb=" N   VAL B 127 "
        pdb=" CA  VAL B 127 "
        pdb=" C   VAL B 127 "
      ideal   model   delta    sigma   weight residual
     113.71  107.35    6.36 9.50e-01 1.11e+00 4.48e+01
  angle pdb=" C   ASP A 445 "
        pdb=" CA  ASP A 445 "
        pdb=" CB  ASP A 445 "
      ideal   model   delta    sigma   weight residual
     116.54  109.95    6.59 1.15e+00 7.56e-01 3.28e+01
  angle pdb=" N   GLU B 277 "
        pdb=" CA  GLU B 277 "
        pdb=" C   GLU B 277 "
      ideal   model   delta    sigma   weight residual
     110.35  104.00    6.35 1.36e+00 5.41e-01 2.18e+01
  angle pdb=" C   ASP B 402 "
        pdb=" N   GLU B 403 "
        pdb=" CA  GLU B 403 "
      ideal   model   delta    sigma   weight residual
     121.80  132.13  -10.33 2.44e+00 1.68e-01 1.79e+01
  angle pdb=" CA  TYR B 456 "
        pdb=" CB  TYR B 456 "
        pdb=" CG  TYR B 456 "
      ideal   model   delta    sigma   weight residual
     113.90  120.41   -6.51 1.80e+00 3.09e-01 1.31e+01
  ... (remaining 12201 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.86: 4696
       17.86 -    35.71: 577
       35.71 -    53.57: 112
       53.57 -    71.42: 34
       71.42 -    89.28: 9
  Dihedral angle restraints: 5428
    sinusoidal: 2152
      harmonic: 3276
  Sorted by residual:
  dihedral pdb=" CA  LEU A 502 "
           pdb=" C   LEU A 502 "
           pdb=" N   ASP A 503 "
           pdb=" CA  ASP A 503 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  155.80   24.20     0      5.00e+00 4.00e-02 2.34e+01
  dihedral pdb=" CA  LYS A 165 "
           pdb=" C   LYS A 165 "
           pdb=" N   LEU A 166 "
           pdb=" CA  LEU A 166 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -159.23  -20.77     0      5.00e+00 4.00e-02 1.72e+01
  dihedral pdb=" CA  MET B  59 "
           pdb=" C   MET B  59 "
           pdb=" N   SER B  60 "
           pdb=" CA  SER B  60 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -159.41  -20.59     0      5.00e+00 4.00e-02 1.70e+01
  ... (remaining 5425 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.036: 997
       0.036 -    0.072: 350
       0.072 -    0.108: 84
       0.108 -    0.144: 29
       0.144 -    0.180: 4
  Chirality restraints: 1464
  Sorted by residual:
  chirality pdb=" CG  LEU B 171 "
            pdb=" CB  LEU B 171 "
            pdb=" CD1 LEU B 171 "
            pdb=" CD2 LEU B 171 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.41   -0.18 2.00e-01 2.50e+01 8.06e-01
  chirality pdb=" CA  GLU B 277 "
            pdb=" N   GLU B 277 "
            pdb=" C   GLU B 277 "
            pdb=" CB  GLU B 277 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.68   -0.17 2.00e-01 2.50e+01 7.23e-01
  chirality pdb=" CA  SER A 508 "
            pdb=" N   SER A 508 "
            pdb=" C   SER A 508 "
            pdb=" CB  SER A 508 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.36    0.15 2.00e-01 2.50e+01 5.74e-01
  ... (remaining 1461 not shown)

  Planarity restraints: 1524
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL A 263 "    0.012 2.00e-02 2.50e+03   2.50e-02 6.23e+00
        pdb=" C   VAL A 263 "   -0.043 2.00e-02 2.50e+03
        pdb=" O   VAL A 263 "    0.016 2.00e-02 2.50e+03
        pdb=" N   ALA A 264 "    0.014 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ALA A 260 "   -0.011 2.00e-02 2.50e+03   2.18e-02 4.74e+00
        pdb=" C   ALA A 260 "    0.038 2.00e-02 2.50e+03
        pdb=" O   ALA A 260 "   -0.014 2.00e-02 2.50e+03
        pdb=" N   ALA A 261 "   -0.013 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ALA A 264 "   -0.010 2.00e-02 2.50e+03   2.10e-02 4.42e+00
        pdb=" C   ALA A 264 "    0.036 2.00e-02 2.50e+03
        pdb=" O   ALA A 264 "   -0.014 2.00e-02 2.50e+03
        pdb=" N   VAL A 265 "   -0.012 2.00e-02 2.50e+03
  ... (remaining 1521 not shown)

  Histogram of nonbonded interaction distances:
        2.11 -     2.67: 129
        2.67 -     3.22: 9042
        3.22 -     3.78: 13969
        3.78 -     4.34: 17650
        4.34 -     4.90: 29123
  Nonbonded interactions: 69913
  Sorted by model distance:
  nonbonded pdb=" OG1 THR B  40 "
            pdb=" OG1 THR B 147 "
     model   vdw
     2.108 3.040
  nonbonded pdb=" O   ASN B 466 "
            pdb=" OG1 THR B 470 "
     model   vdw
     2.186 3.040
  nonbonded pdb=" O   LEU B 464 "
            pdb=" CD1 LEU B 464 "
     model   vdw
     2.202 3.460
  nonbonded pdb=" NH1 ARG A 214 "
            pdb=" OH  TYR B 419 "
     model   vdw
     2.238 3.120
  nonbonded pdb=" OG  SER B  43 "
            pdb=" NE2 GLN B  77 "
     model   vdw
     2.254 3.120
  ... (remaining 69908 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.01
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.040
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.160
  Check model and map are aligned:         0.040
  Set scattering table:                    0.030
  Process input model:                     9.420
  Find NCS groups from input model:        0.090
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.340
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   12.150
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7674
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   9014  Z= 0.159
  Angle     :  0.728  10.329  12206  Z= 0.393
  Chirality :  0.041   0.180   1464
  Planarity :  0.004   0.042   1524
  Dihedral  : 16.583  89.277   3324
  Min Nonbonded Distance : 2.108

Molprobity Statistics.
  All-atom Clashscore : 13.61
  Ramachandran Plot:
    Outliers :  0.44 %
    Allowed  :  6.84 %
    Favored  : 92.72 %
  Rotamer:
    Outliers :  2.49 %
    Allowed  : 23.76 %
    Favored  : 73.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.30 (0.26), residues: 1140
  helix:  1.49 (0.19), residues: 742
  sheet:  0.11 (0.59), residues: 82
  loop : -3.06 (0.31), residues: 316

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 495 
 TYR   0.010   0.001   TYR A 419 
 PHE   0.017   0.001   PHE A  57 
 TRP   0.003   0.001   TRP B 413 
 HIS   0.004   0.001   HIS A 560 

Details of bonding type rmsd
  covalent geometry    : bond        0.00307 ( 9014)
  covalent geometry    : angle       0.72836 (12206)
  hydrogen bonds       : bond        0.12877 (  591)
  hydrogen bonds       : angle       5.83788 ( 1755)

*********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  2280 Ramachandran restraints generated.
    1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2280 Ramachandran restraints generated.
    1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  124 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 100
  time to evaluate  : 0.397 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  388 GLU cc_start: 0.8168 (tt0) cc_final: 0.7823 (tt0)
REVERT: A  448 ILE cc_start: 0.5656 (OUTLIER) cc_final: 0.4987 (mp)
REVERT: A  464 LEU cc_start: 0.5220 (OUTLIER) cc_final: 0.4566 (tp)
REVERT: B   94 LYS cc_start: 0.8079 (mmmm) cc_final: 0.7287 (ttmt)
REVERT: B  180 ILE cc_start: 0.8471 (mm) cc_final: 0.8216 (mt)
REVERT: B  181 LEU cc_start: 0.7609 (OUTLIER) cc_final: 0.7184 (mp)
  outliers start: 24
  outliers final: 20
  residues processed: 117
  average time/residue: 0.0756
  time to fit residues: 13.5459
Evaluate side-chains
  119 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 96
  time to evaluate  : 0.386 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   46 ILE
Chi-restraints excluded: chain A residue  112 VAL
Chi-restraints excluded: chain A residue  123 THR
Chi-restraints excluded: chain A residue  147 THR
Chi-restraints excluded: chain A residue  149 ILE
Chi-restraints excluded: chain A residue  176 LEU
Chi-restraints excluded: chain A residue  208 GLN
Chi-restraints excluded: chain A residue  210 LEU
Chi-restraints excluded: chain A residue  220 ASN
Chi-restraints excluded: chain A residue  295 MET
Chi-restraints excluded: chain A residue  445 ASP
Chi-restraints excluded: chain A residue  448 ILE
Chi-restraints excluded: chain A residue  464 LEU
Chi-restraints excluded: chain B residue   22 THR
Chi-restraints excluded: chain B residue  112 VAL
Chi-restraints excluded: chain B residue  176 LEU
Chi-restraints excluded: chain B residue  181 LEU
Chi-restraints excluded: chain B residue  239 LEU
Chi-restraints excluded: chain B residue  248 SER
Chi-restraints excluded: chain B residue  310 SER
Chi-restraints excluded: chain B residue  387 LEU
Chi-restraints excluded: chain B residue  437 TYR
Chi-restraints excluded: chain B residue  524 LEU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 108 optimal weight:   10.0000
   chunk 49 optimal weight:    0.0870
   chunk 97 optimal weight:    8.9990
   chunk 113 optimal weight:    9.9990
   chunk 53 optimal weight:   20.0000
   chunk 5 optimal weight:    2.9990
   chunk 33 optimal weight:    5.9990
   chunk 65 optimal weight:    0.8980
   chunk 62 optimal weight:    0.6980
   chunk 51 optimal weight:    8.9990
   chunk 100 optimal weight:    0.0050
   overall best weight:    0.9374

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
A 141 HIS
** B 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4723 r_free = 0.4723 target = 0.229067 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.4209 r_free = 0.4209 target = 0.168891 restraints weight = 11208.893|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.4101 r_free = 0.4101 target = 0.166189 restraints weight = 10488.132|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.4114 r_free = 0.4114 target = 0.167822 restraints weight = 9593.980|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.4126 r_free = 0.4126 target = 0.169226 restraints weight = 5033.533|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.4130 r_free = 0.4130 target = 0.169906 restraints weight = 4344.324|
|-----------------------------------------------------------------------------|
r_work (final): 0.4090
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7472
moved from start:          0.0891

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   9014  Z= 0.145
  Angle     :  0.632  12.072  12206  Z= 0.320
  Chirality :  0.041   0.144   1464
  Planarity :  0.004   0.048   1524
  Dihedral  :  8.341  58.787   1285
  Min Nonbonded Distance : 2.471

Molprobity Statistics.
  All-atom Clashscore : 10.07
  Ramachandran Plot:
    Outliers :  0.26 %
    Allowed  :  6.23 %
    Favored  : 93.51 %
  Rotamer:
    Outliers :  4.46 %
    Allowed  : 22.20 %
    Favored  : 73.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.82 (0.26), residues: 1140
  helix:  1.95 (0.19), residues: 748
  sheet: -0.23 (0.57), residues: 92
  loop : -3.05 (0.32), residues: 300

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 214 
 TYR   0.011   0.001   TYR A 408 
 PHE   0.014   0.001   PHE A  57 
 TRP   0.004   0.001   TRP A 164 
 HIS   0.005   0.001   HIS A 560 

Details of bonding type rmsd
  covalent geometry    : bond        0.00313 ( 9014)
  covalent geometry    : angle       0.63236 (12206)
  hydrogen bonds       : bond        0.04752 (  591)
  hydrogen bonds       : angle       4.47999 ( 1755)

*********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  2280 Ramachandran restraints generated.
    1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2280 Ramachandran restraints generated.
    1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  147 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 104
  time to evaluate  : 0.433 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  109 LYS cc_start: 0.8928 (mmtp) cc_final: 0.8552 (mmmt)
REVERT: A  448 ILE cc_start: 0.5694 (OUTLIER) cc_final: 0.4914 (mp)
REVERT: A  464 LEU cc_start: 0.4941 (OUTLIER) cc_final: 0.4466 (tp)
REVERT: B   94 LYS cc_start: 0.8166 (mmmm) cc_final: 0.7372 (ttmt)
REVERT: B  180 ILE cc_start: 0.8394 (mm) cc_final: 0.8142 (mt)
REVERT: B  181 LEU cc_start: 0.7779 (OUTLIER) cc_final: 0.7374 (mp)
REVERT: B  317 MET cc_start: 0.8308 (tpp) cc_final: 0.7600 (mtt)
REVERT: B  564 MET cc_start: 0.1547 (mmm) cc_final: 0.1305 (mmm)
  outliers start: 43
  outliers final: 27
  residues processed: 140
  average time/residue: 0.0853
  time to fit residues: 17.6480
Evaluate side-chains
  128 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 98
  time to evaluate  : 0.331 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   43 SER
Chi-restraints excluded: chain A residue   96 ILE
Chi-restraints excluded: chain A residue  108 ILE
Chi-restraints excluded: chain A residue  110 LEU
Chi-restraints excluded: chain A residue  112 VAL
Chi-restraints excluded: chain A residue  132 MET
Chi-restraints excluded: chain A residue  147 THR
Chi-restraints excluded: chain A residue  174 VAL
Chi-restraints excluded: chain A residue  195 THR
Chi-restraints excluded: chain A residue  199 THR
Chi-restraints excluded: chain A residue  208 GLN
Chi-restraints excluded: chain A residue  220 ASN
Chi-restraints excluded: chain A residue  236 LEU
Chi-restraints excluded: chain A residue  310 SER
Chi-restraints excluded: chain A residue  448 ILE
Chi-restraints excluded: chain A residue  464 LEU
Chi-restraints excluded: chain A residue  524 LEU
Chi-restraints excluded: chain A residue  532 VAL
Chi-restraints excluded: chain B residue  110 LEU
Chi-restraints excluded: chain B residue  112 VAL
Chi-restraints excluded: chain B residue  127 VAL
Chi-restraints excluded: chain B residue  128 THR
Chi-restraints excluded: chain B residue  156 LEU
Chi-restraints excluded: chain B residue  181 LEU
Chi-restraints excluded: chain B residue  195 THR
Chi-restraints excluded: chain B residue  199 THR
Chi-restraints excluded: chain B residue  239 LEU
Chi-restraints excluded: chain B residue  402 ASP
Chi-restraints excluded: chain B residue  437 TYR
Chi-restraints excluded: chain B residue  448 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 28 optimal weight:    1.9990
   chunk 43 optimal weight:    0.0670
   chunk 42 optimal weight:    6.9990
   chunk 90 optimal weight:    0.7980
   chunk 44 optimal weight:    4.9990
   chunk 47 optimal weight:    8.9990
   chunk 18 optimal weight:    5.9990
   chunk 40 optimal weight:    5.9990
   chunk 10 optimal weight:    0.9990
   chunk 32 optimal weight:    0.2980
   chunk 102 optimal weight:    0.5980
   overall best weight:    0.5520

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
B 220 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4660 r_free = 0.4660 target = 0.223647 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 65)----------------|
| r_work = 0.3819 r_free = 0.3819 target = 0.139423 restraints weight = 11113.251|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 52)----------------|
| r_work = 0.3882 r_free = 0.3882 target = 0.144742 restraints weight = 5438.353|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 54)----------------|
| r_work = 0.3917 r_free = 0.3917 target = 0.147895 restraints weight = 3671.391|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3934 r_free = 0.3934 target = 0.149486 restraints weight = 2987.700|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3942 r_free = 0.3942 target = 0.150226 restraints weight = 2689.798|
|-----------------------------------------------------------------------------|
r_work (final): 0.3892
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7626
moved from start:          0.1261

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   9014  Z= 0.126
  Angle     :  0.611   9.909  12206  Z= 0.307
  Chirality :  0.040   0.147   1464
  Planarity :  0.004   0.044   1524
  Dihedral  :  7.715  58.863   1262
  Min Nonbonded Distance : 2.487

Molprobity Statistics.
  All-atom Clashscore : 10.07
  Ramachandran Plot:
    Outliers :  0.26 %
    Allowed  :  6.32 %
    Favored  : 93.42 %
  Rotamer:
    Outliers :  3.53 %
    Allowed  : 24.07 %
    Favored  : 72.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.08 (0.26), residues: 1140
  helix:  2.17 (0.19), residues: 750
  sheet: -0.00 (0.58), residues: 90
  loop : -3.06 (0.32), residues: 300

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 495 
 TYR   0.012   0.001   TYR A 408 
 PHE   0.012   0.001   PHE A 348 
 TRP   0.005   0.001   TRP A 164 
 HIS   0.005   0.001   HIS A 560 

Details of bonding type rmsd
  covalent geometry    : bond        0.00258 ( 9014)
  covalent geometry    : angle       0.61080 (12206)
  hydrogen bonds       : bond        0.04323 (  591)
  hydrogen bonds       : angle       4.25133 ( 1755)

*********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  2280 Ramachandran restraints generated.
    1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2280 Ramachandran restraints generated.
    1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  143 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 109
  time to evaluate  : 0.353 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  109 LYS cc_start: 0.8913 (mmtp) cc_final: 0.8426 (mmmt)
REVERT: A  317 MET cc_start: 0.8481 (tpp) cc_final: 0.8265 (mmt)
REVERT: A  411 GLU cc_start: 0.9083 (pp20) cc_final: 0.8881 (pp20)
REVERT: A  464 LEU cc_start: 0.5244 (OUTLIER) cc_final: 0.4875 (tp)
REVERT: B   94 LYS cc_start: 0.7995 (mmmm) cc_final: 0.7209 (ttmt)
REVERT: B  169 LEU cc_start: 0.8618 (OUTLIER) cc_final: 0.8413 (mm)
REVERT: B  181 LEU cc_start: 0.7531 (OUTLIER) cc_final: 0.7170 (mp)
REVERT: B  317 MET cc_start: 0.8187 (tpp) cc_final: 0.7889 (mtt)
  outliers start: 34
  outliers final: 21
  residues processed: 137
  average time/residue: 0.0853
  time to fit residues: 17.0686
Evaluate side-chains
  124 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 100
  time to evaluate  : 0.325 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   43 SER
Chi-restraints excluded: chain A residue   96 ILE
Chi-restraints excluded: chain A residue  108 ILE
Chi-restraints excluded: chain A residue  110 LEU
Chi-restraints excluded: chain A residue  112 VAL
Chi-restraints excluded: chain A residue  132 MET
Chi-restraints excluded: chain A residue  147 THR
Chi-restraints excluded: chain A residue  174 VAL
Chi-restraints excluded: chain A residue  210 LEU
Chi-restraints excluded: chain A residue  220 ASN
Chi-restraints excluded: chain A residue  236 LEU
Chi-restraints excluded: chain A residue  464 LEU
Chi-restraints excluded: chain B residue  110 LEU
Chi-restraints excluded: chain B residue  127 VAL
Chi-restraints excluded: chain B residue  143 SER
Chi-restraints excluded: chain B residue  156 LEU
Chi-restraints excluded: chain B residue  169 LEU
Chi-restraints excluded: chain B residue  181 LEU
Chi-restraints excluded: chain B residue  199 THR
Chi-restraints excluded: chain B residue  239 LEU
Chi-restraints excluded: chain B residue  356 ILE
Chi-restraints excluded: chain B residue  387 LEU
Chi-restraints excluded: chain B residue  437 TYR
Chi-restraints excluded: chain B residue  448 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 100 optimal weight:   20.0000
   chunk 24 optimal weight:    0.3980
   chunk 92 optimal weight:    7.9990
   chunk 90 optimal weight:    4.9990
   chunk 14 optimal weight:    0.6980
   chunk 48 optimal weight:    0.7980
   chunk 37 optimal weight:    6.9990
   chunk 62 optimal weight:    8.9990
   chunk 15 optimal weight:    0.7980
   chunk 71 optimal weight:    0.8980
   chunk 36 optimal weight:   20.0000
   overall best weight:    0.7180

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
B 220 ASN
B 434 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4520 r_free = 0.4520 target = 0.215372 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3660 r_free = 0.3660 target = 0.131311 restraints weight = 11190.812|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3657 r_free = 0.3657 target = 0.130956 restraints weight = 8292.575|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3680 r_free = 0.3680 target = 0.133374 restraints weight = 5210.883|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3681 r_free = 0.3681 target = 0.133381 restraints weight = 4196.790|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3701 r_free = 0.3701 target = 0.135327 restraints weight = 3929.300|
|-----------------------------------------------------------------------------|
r_work (final): 0.3661
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7607
moved from start:          0.1505

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   9014  Z= 0.127
  Angle     :  0.611   9.893  12206  Z= 0.303
  Chirality :  0.040   0.147   1464
  Planarity :  0.004   0.044   1524
  Dihedral  :  7.273  59.252   1256
  Min Nonbonded Distance : 2.449

Molprobity Statistics.
  All-atom Clashscore : 9.68
  Ramachandran Plot:
    Outliers :  0.26 %
    Allowed  :  6.93 %
    Favored  : 92.81 %
  Rotamer:
    Outliers :  4.98 %
    Allowed  : 24.07 %
    Favored  : 70.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.17 (0.26), residues: 1140
  helix:  2.26 (0.19), residues: 750
  sheet: -0.09 (0.59), residues: 90
  loop : -3.04 (0.32), residues: 300

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 414 
 TYR   0.012   0.001   TYR A 408 
 PHE   0.013   0.001   PHE A 348 
 TRP   0.012   0.001   TRP A 104 
 HIS   0.004   0.001   HIS A 560 

Details of bonding type rmsd
  covalent geometry    : bond        0.00266 ( 9014)
  covalent geometry    : angle       0.61142 (12206)
  hydrogen bonds       : bond        0.04212 (  591)
  hydrogen bonds       : angle       4.17641 ( 1755)

*********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  2280 Ramachandran restraints generated.
    1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2280 Ramachandran restraints generated.
    1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  158 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 48
    poor density    : 110
  time to evaluate  : 0.339 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  109 LYS cc_start: 0.8913 (mmtp) cc_final: 0.8428 (mmmt)
REVERT: A  317 MET cc_start: 0.8621 (tpp) cc_final: 0.8171 (mmt)
REVERT: A  448 ILE cc_start: 0.5147 (OUTLIER) cc_final: 0.4463 (mp)
REVERT: A  464 LEU cc_start: 0.5353 (OUTLIER) cc_final: 0.5056 (tp)
REVERT: B   94 LYS cc_start: 0.7991 (mmmm) cc_final: 0.7212 (ttmt)
REVERT: B  114 TYR cc_start: 0.8431 (t80) cc_final: 0.8162 (t80)
REVERT: B  167 THR cc_start: 0.5025 (OUTLIER) cc_final: 0.4450 (p)
REVERT: B  181 LEU cc_start: 0.7406 (OUTLIER) cc_final: 0.7053 (mp)
REVERT: B  434 ASN cc_start: 0.7354 (m-40) cc_final: 0.7148 (m-40)
  outliers start: 48
  outliers final: 26
  residues processed: 150
  average time/residue: 0.0822
  time to fit residues: 18.2465
Evaluate side-chains
  134 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 104
  time to evaluate  : 0.371 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   96 ILE
Chi-restraints excluded: chain A residue  108 ILE
Chi-restraints excluded: chain A residue  110 LEU
Chi-restraints excluded: chain A residue  112 VAL
Chi-restraints excluded: chain A residue  132 MET
Chi-restraints excluded: chain A residue  147 THR
Chi-restraints excluded: chain A residue  174 VAL
Chi-restraints excluded: chain A residue  181 LEU
Chi-restraints excluded: chain A residue  210 LEU
Chi-restraints excluded: chain A residue  220 ASN
Chi-restraints excluded: chain A residue  236 LEU
Chi-restraints excluded: chain A residue  320 ILE
Chi-restraints excluded: chain A residue  448 ILE
Chi-restraints excluded: chain A residue  464 LEU
Chi-restraints excluded: chain A residue  524 LEU
Chi-restraints excluded: chain A residue  530 THR
Chi-restraints excluded: chain B residue  110 LEU
Chi-restraints excluded: chain B residue  143 SER
Chi-restraints excluded: chain B residue  156 LEU
Chi-restraints excluded: chain B residue  167 THR
Chi-restraints excluded: chain B residue  181 LEU
Chi-restraints excluded: chain B residue  199 THR
Chi-restraints excluded: chain B residue  210 LEU
Chi-restraints excluded: chain B residue  239 LEU
Chi-restraints excluded: chain B residue  311 ILE
Chi-restraints excluded: chain B residue  356 ILE
Chi-restraints excluded: chain B residue  387 LEU
Chi-restraints excluded: chain B residue  417 ILE
Chi-restraints excluded: chain B residue  437 TYR
Chi-restraints excluded: chain B residue  448 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 62 optimal weight:    7.9990
   chunk 6 optimal weight:    3.9990
   chunk 51 optimal weight:   10.0000
   chunk 53 optimal weight:    9.9990
   chunk 80 optimal weight:    3.9990
   chunk 73 optimal weight:    1.9990
   chunk 16 optimal weight:    3.9990
   chunk 104 optimal weight:    8.9990
   chunk 95 optimal weight:   10.0000
   chunk 83 optimal weight:    2.9990
   chunk 96 optimal weight:    8.9990
   overall best weight:    3.3990

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
B 220 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4584 r_free = 0.4584 target = 0.214519 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3681 r_free = 0.3681 target = 0.129014 restraints weight = 11452.469|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3708 r_free = 0.3708 target = 0.131434 restraints weight = 7281.615|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3725 r_free = 0.3725 target = 0.133111 restraints weight = 4749.291|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3726 r_free = 0.3726 target = 0.133304 restraints weight = 4095.422|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3731 r_free = 0.3731 target = 0.133718 restraints weight = 4129.251|
|-----------------------------------------------------------------------------|
r_work (final): 0.3673
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7934
moved from start:          0.1890

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.064   9014  Z= 0.299
  Angle     :  0.795  10.076  12206  Z= 0.394
  Chirality :  0.046   0.167   1464
  Planarity :  0.005   0.068   1524
  Dihedral  :  7.641  57.485   1256
  Min Nonbonded Distance : 2.411

Molprobity Statistics.
  All-atom Clashscore : 12.89
  Ramachandran Plot:
    Outliers :  0.26 %
    Allowed  :  7.37 %
    Favored  : 92.37 %
  Rotamer:
    Outliers :  5.81 %
    Allowed  : 24.38 %
    Favored  : 69.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.67 (0.26), residues: 1140
  helix:  1.82 (0.19), residues: 748
  sheet: -0.42 (0.57), residues: 90
  loop : -2.99 (0.33), residues: 302

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 495 
 TYR   0.010   0.002   TYR B  26 
 PHE   0.022   0.002   PHE A  57 
 TRP   0.006   0.001   TRP A 104 
 HIS   0.005   0.001   HIS A 560 

Details of bonding type rmsd
  covalent geometry    : bond        0.00715 ( 9014)
  covalent geometry    : angle       0.79479 (12206)
  hydrogen bonds       : bond        0.05234 (  591)
  hydrogen bonds       : angle       4.53409 ( 1755)

*********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  2280 Ramachandran restraints generated.
    1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2280 Ramachandran restraints generated.
    1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  152 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 56
    poor density    : 96
  time to evaluate  : 0.306 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  109 LYS cc_start: 0.8951 (mmtp) cc_final: 0.8495 (mmmt)
REVERT: A  317 MET cc_start: 0.8632 (tpp) cc_final: 0.8074 (mtt)
REVERT: A  464 LEU cc_start: 0.5396 (OUTLIER) cc_final: 0.4795 (tp)
REVERT: A  525 MET cc_start: 0.3238 (ppp) cc_final: 0.2621 (ppp)
REVERT: B  176 LEU cc_start: 0.6212 (OUTLIER) cc_final: 0.5939 (tt)
REVERT: B  181 LEU cc_start: 0.7917 (OUTLIER) cc_final: 0.7456 (mp)
REVERT: B  225 GLU cc_start: 0.8645 (mm-30) cc_final: 0.8232 (mm-30)
REVERT: B  388 GLU cc_start: 0.8364 (mt-10) cc_final: 0.7991 (mt-10)
REVERT: B  391 TYR cc_start: 0.8849 (m-10) cc_final: 0.8556 (m-10)
REVERT: B  448 ILE cc_start: 0.5147 (OUTLIER) cc_final: 0.4859 (mt)
  outliers start: 56
  outliers final: 34
  residues processed: 142
  average time/residue: 0.0774
  time to fit residues: 16.5818
Evaluate side-chains
  126 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 88
  time to evaluate  : 0.358 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   22 THR
Chi-restraints excluded: chain A residue   96 ILE
Chi-restraints excluded: chain A residue  108 ILE
Chi-restraints excluded: chain A residue  112 VAL
Chi-restraints excluded: chain A residue  123 THR
Chi-restraints excluded: chain A residue  147 THR
Chi-restraints excluded: chain A residue  153 ILE
Chi-restraints excluded: chain A residue  174 VAL
Chi-restraints excluded: chain A residue  195 THR
Chi-restraints excluded: chain A residue  210 LEU
Chi-restraints excluded: chain A residue  220 ASN
Chi-restraints excluded: chain A residue  236 LEU
Chi-restraints excluded: chain A residue  310 SER
Chi-restraints excluded: chain A residue  387 LEU
Chi-restraints excluded: chain A residue  464 LEU
Chi-restraints excluded: chain A residue  524 LEU
Chi-restraints excluded: chain A residue  533 ILE
Chi-restraints excluded: chain B residue   46 ILE
Chi-restraints excluded: chain B residue   96 ILE
Chi-restraints excluded: chain B residue  110 LEU
Chi-restraints excluded: chain B residue  112 VAL
Chi-restraints excluded: chain B residue  127 VAL
Chi-restraints excluded: chain B residue  128 THR
Chi-restraints excluded: chain B residue  143 SER
Chi-restraints excluded: chain B residue  176 LEU
Chi-restraints excluded: chain B residue  181 LEU
Chi-restraints excluded: chain B residue  195 THR
Chi-restraints excluded: chain B residue  199 THR
Chi-restraints excluded: chain B residue  236 LEU
Chi-restraints excluded: chain B residue  239 LEU
Chi-restraints excluded: chain B residue  310 SER
Chi-restraints excluded: chain B residue  341 ILE
Chi-restraints excluded: chain B residue  356 ILE
Chi-restraints excluded: chain B residue  387 LEU
Chi-restraints excluded: chain B residue  437 TYR
Chi-restraints excluded: chain B residue  448 ILE
Chi-restraints excluded: chain B residue  464 LEU
Chi-restraints excluded: chain B residue  524 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 112 optimal weight:    5.9990
   chunk 75 optimal weight:    0.8980
   chunk 19 optimal weight:    0.9980
   chunk 64 optimal weight:    0.7980
   chunk 40 optimal weight:    9.9990
   chunk 5 optimal weight:    3.9990
   chunk 73 optimal weight:    0.4980
   chunk 86 optimal weight:    0.7980
   chunk 33 optimal weight:    5.9990
   chunk 13 optimal weight:    0.6980
   chunk 39 optimal weight:    0.0070
   overall best weight:    0.5598

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
B 220 ASN
** B 560 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4499 r_free = 0.4499 target = 0.213040 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3611 r_free = 0.3611 target = 0.127921 restraints weight = 11160.013|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3621 r_free = 0.3621 target = 0.128444 restraints weight = 7536.438|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3636 r_free = 0.3636 target = 0.130112 restraints weight = 4848.093|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3639 r_free = 0.3639 target = 0.130515 restraints weight = 4349.258|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3646 r_free = 0.3646 target = 0.131050 restraints weight = 4012.714|
|-----------------------------------------------------------------------------|
r_work (final): 0.3603
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7649
moved from start:          0.1871

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   9014  Z= 0.129
  Angle     :  0.627  10.182  12206  Z= 0.314
  Chirality :  0.041   0.171   1464
  Planarity :  0.004   0.066   1524
  Dihedral  :  7.445  57.353   1256
  Min Nonbonded Distance : 2.362

Molprobity Statistics.
  All-atom Clashscore : 10.79
  Ramachandran Plot:
    Outliers :  0.26 %
    Allowed  :  6.93 %
    Favored  : 92.81 %
  Rotamer:
    Outliers :  4.15 %
    Allowed  : 25.52 %
    Favored  : 70.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.01 (0.26), residues: 1140
  helix:  2.14 (0.19), residues: 748
  sheet: -0.39 (0.57), residues: 90
  loop : -3.00 (0.33), residues: 302

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 214 
 TYR   0.011   0.001   TYR A 408 
 PHE   0.016   0.001   PHE A  57 
 TRP   0.004   0.001   TRP A 104 
 HIS   0.017   0.002   HIS B 560 

Details of bonding type rmsd
  covalent geometry    : bond        0.00265 ( 9014)
  covalent geometry    : angle       0.62652 (12206)
  hydrogen bonds       : bond        0.04364 (  591)
  hydrogen bonds       : angle       4.27323 ( 1755)

*********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  2280 Ramachandran restraints generated.
    1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2280 Ramachandran restraints generated.
    1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  144 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 104
  time to evaluate  : 0.394 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  109 LYS cc_start: 0.8809 (mmtp) cc_final: 0.8330 (mmmt)
REVERT: A  525 MET cc_start: 0.2961 (ppp) cc_final: 0.2260 (ppp)
REVERT: B   94 LYS cc_start: 0.8018 (mmmm) cc_final: 0.7193 (ttmt)
REVERT: B  181 LEU cc_start: 0.7509 (OUTLIER) cc_final: 0.7105 (mp)
REVERT: B  225 GLU cc_start: 0.8573 (mm-30) cc_final: 0.8193 (mm-30)
REVERT: B  391 TYR cc_start: 0.8773 (m-10) cc_final: 0.8435 (m-10)
REVERT: B  400 LEU cc_start: 0.7698 (OUTLIER) cc_final: 0.7440 (tp)
  outliers start: 40
  outliers final: 21
  residues processed: 138
  average time/residue: 0.0780
  time to fit residues: 16.0979
Evaluate side-chains
  120 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 97
  time to evaluate  : 0.336 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   96 ILE
Chi-restraints excluded: chain A residue  108 ILE
Chi-restraints excluded: chain A residue  112 VAL
Chi-restraints excluded: chain A residue  147 THR
Chi-restraints excluded: chain A residue  174 VAL
Chi-restraints excluded: chain A residue  210 LEU
Chi-restraints excluded: chain A residue  220 ASN
Chi-restraints excluded: chain A residue  310 SER
Chi-restraints excluded: chain A residue  320 ILE
Chi-restraints excluded: chain A residue  387 LEU
Chi-restraints excluded: chain A residue  524 LEU
Chi-restraints excluded: chain B residue  110 LEU
Chi-restraints excluded: chain B residue  143 SER
Chi-restraints excluded: chain B residue  181 LEU
Chi-restraints excluded: chain B residue  199 THR
Chi-restraints excluded: chain B residue  239 LEU
Chi-restraints excluded: chain B residue  341 ILE
Chi-restraints excluded: chain B residue  387 LEU
Chi-restraints excluded: chain B residue  400 LEU
Chi-restraints excluded: chain B residue  420 VAL
Chi-restraints excluded: chain B residue  431 ILE
Chi-restraints excluded: chain B residue  448 ILE
Chi-restraints excluded: chain B residue  464 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 0 optimal weight:    7.9990
   chunk 27 optimal weight:    0.0050
   chunk 90 optimal weight:    6.9990
   chunk 7 optimal weight:    0.6980
   chunk 101 optimal weight:    8.9990
   chunk 51 optimal weight:    8.9990
   chunk 98 optimal weight:   10.0000
   chunk 95 optimal weight:    2.9990
   chunk 64 optimal weight:    0.7980
   chunk 40 optimal weight:    9.9990
   chunk 20 optimal weight:    0.9980
   overall best weight:    1.0996

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
B 220 ASN
** B 560 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4632 r_free = 0.4632 target = 0.220180 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3760 r_free = 0.3760 target = 0.135316 restraints weight = 11374.437|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3812 r_free = 0.3812 target = 0.140118 restraints weight = 5921.789|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3836 r_free = 0.3836 target = 0.142146 restraints weight = 4101.888|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3842 r_free = 0.3842 target = 0.142909 restraints weight = 3323.264|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3849 r_free = 0.3849 target = 0.143394 restraints weight = 3386.045|
|-----------------------------------------------------------------------------|
r_work (final): 0.3786
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7790
moved from start:          0.2004

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   9014  Z= 0.146
  Angle     :  0.647   9.801  12206  Z= 0.323
  Chirality :  0.041   0.145   1464
  Planarity :  0.004   0.060   1524
  Dihedral  :  7.084  56.073   1252
  Min Nonbonded Distance : 2.354

Molprobity Statistics.
  All-atom Clashscore : 10.46
  Ramachandran Plot:
    Outliers :  0.26 %
    Allowed  :  7.46 %
    Favored  : 92.28 %
  Rotamer:
    Outliers :  4.15 %
    Allowed  : 25.62 %
    Favored  : 70.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.05 (0.26), residues: 1140
  helix:  2.17 (0.19), residues: 748
  sheet: -0.06 (0.62), residues: 78
  loop : -2.98 (0.33), residues: 314

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 414 
 TYR   0.012   0.001   TYR A 408 
 PHE   0.017   0.001   PHE A  57 
 TRP   0.003   0.001   TRP A 104 
 HIS   0.014   0.001   HIS B 560 

Details of bonding type rmsd
  covalent geometry    : bond        0.00323 ( 9014)
  covalent geometry    : angle       0.64710 (12206)
  hydrogen bonds       : bond        0.04328 (  591)
  hydrogen bonds       : angle       4.23125 ( 1755)

*********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  2280 Ramachandran restraints generated.
    1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2280 Ramachandran restraints generated.
    1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  138 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 98
  time to evaluate  : 0.339 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  109 LYS cc_start: 0.8879 (mmtp) cc_final: 0.8400 (mmmt)
REVERT: A  357 LEU cc_start: 0.8277 (OUTLIER) cc_final: 0.8005 (tp)
REVERT: A  525 MET cc_start: 0.3193 (ppp) cc_final: 0.2328 (ppp)
REVERT: B   94 LYS cc_start: 0.8054 (mmmm) cc_final: 0.7274 (ttmt)
REVERT: B  181 LEU cc_start: 0.7709 (OUTLIER) cc_final: 0.7307 (mp)
REVERT: B  225 GLU cc_start: 0.8524 (mm-30) cc_final: 0.8223 (mm-30)
REVERT: B  391 TYR cc_start: 0.8799 (m-10) cc_final: 0.8468 (m-10)
REVERT: B  448 ILE cc_start: 0.5058 (OUTLIER) cc_final: 0.4785 (mt)
  outliers start: 40
  outliers final: 25
  residues processed: 130
  average time/residue: 0.0824
  time to fit residues: 15.7125
Evaluate side-chains
  123 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 95
  time to evaluate  : 0.353 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   22 THR
Chi-restraints excluded: chain A residue   96 ILE
Chi-restraints excluded: chain A residue  108 ILE
Chi-restraints excluded: chain A residue  112 VAL
Chi-restraints excluded: chain A residue  132 MET
Chi-restraints excluded: chain A residue  147 THR
Chi-restraints excluded: chain A residue  174 VAL
Chi-restraints excluded: chain A residue  181 LEU
Chi-restraints excluded: chain A residue  210 LEU
Chi-restraints excluded: chain A residue  220 ASN
Chi-restraints excluded: chain A residue  236 LEU
Chi-restraints excluded: chain A residue  310 SER
Chi-restraints excluded: chain A residue  317 MET
Chi-restraints excluded: chain A residue  357 LEU
Chi-restraints excluded: chain A residue  387 LEU
Chi-restraints excluded: chain B residue  110 LEU
Chi-restraints excluded: chain B residue  143 SER
Chi-restraints excluded: chain B residue  181 LEU
Chi-restraints excluded: chain B residue  195 THR
Chi-restraints excluded: chain B residue  199 THR
Chi-restraints excluded: chain B residue  220 ASN
Chi-restraints excluded: chain B residue  236 LEU
Chi-restraints excluded: chain B residue  239 LEU
Chi-restraints excluded: chain B residue  387 LEU
Chi-restraints excluded: chain B residue  420 VAL
Chi-restraints excluded: chain B residue  431 ILE
Chi-restraints excluded: chain B residue  448 ILE
Chi-restraints excluded: chain B residue  464 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 104 optimal weight:    9.9990
   chunk 91 optimal weight:   20.0000
   chunk 69 optimal weight:    0.5980
   chunk 4 optimal weight:    3.9990
   chunk 3 optimal weight:    0.5980
   chunk 108 optimal weight:    3.9990
   chunk 57 optimal weight:    8.9990
   chunk 29 optimal weight:    0.9990
   chunk 23 optimal weight:    0.9980
   chunk 39 optimal weight:    8.9990
   chunk 51 optimal weight:    0.8980
   overall best weight:    0.8182

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
B 220 ASN
** B 560 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4585 r_free = 0.4585 target = 0.217355 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.4017 r_free = 0.4017 target = 0.154539 restraints weight = 11525.461|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3929 r_free = 0.3929 target = 0.151590 restraints weight = 14583.997|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3953 r_free = 0.3953 target = 0.154293 restraints weight = 11995.186|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3954 r_free = 0.3954 target = 0.154730 restraints weight = 6554.718|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3971 r_free = 0.3971 target = 0.156743 restraints weight = 5793.802|
|-----------------------------------------------------------------------------|
r_work (final): 0.3949
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7426
moved from start:          0.2105

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   9014  Z= 0.134
  Angle     :  0.641   9.746  12206  Z= 0.318
  Chirality :  0.040   0.139   1464
  Planarity :  0.004   0.056   1524
  Dihedral  :  7.010  56.860   1252
  Min Nonbonded Distance : 2.366

Molprobity Statistics.
  All-atom Clashscore : 10.18
  Ramachandran Plot:
    Outliers :  0.26 %
    Allowed  :  6.84 %
    Favored  : 92.89 %
  Rotamer:
    Outliers :  3.84 %
    Allowed  : 25.83 %
    Favored  : 70.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.14 (0.26), residues: 1140
  helix:  2.19 (0.19), residues: 754
  sheet: -0.33 (0.58), residues: 90
  loop : -2.88 (0.34), residues: 296

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 414 
 TYR   0.011   0.001   TYR A 408 
 PHE   0.016   0.001   PHE A  57 
 TRP   0.003   0.001   TRP A 104 
 HIS   0.012   0.001   HIS B 560 

Details of bonding type rmsd
  covalent geometry    : bond        0.00290 ( 9014)
  covalent geometry    : angle       0.64071 (12206)
  hydrogen bonds       : bond        0.04196 (  591)
  hydrogen bonds       : angle       4.19888 ( 1755)

*********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  2280 Ramachandran restraints generated.
    1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2280 Ramachandran restraints generated.
    1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  141 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 104
  time to evaluate  : 0.341 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  109 LYS cc_start: 0.8890 (mmtp) cc_final: 0.8472 (mmmt)
REVERT: A  525 MET cc_start: 0.3393 (ppp) cc_final: 0.2484 (ppp)
REVERT: B   94 LYS cc_start: 0.8161 (mmmm) cc_final: 0.7398 (ttmt)
REVERT: B  118 ASN cc_start: 0.8274 (t0) cc_final: 0.7940 (t0)
REVERT: B  181 LEU cc_start: 0.7706 (OUTLIER) cc_final: 0.7340 (mp)
REVERT: B  400 LEU cc_start: 0.6959 (OUTLIER) cc_final: 0.6669 (tp)
REVERT: B  448 ILE cc_start: 0.5764 (OUTLIER) cc_final: 0.5518 (mt)
  outliers start: 37
  outliers final: 24
  residues processed: 135
  average time/residue: 0.0812
  time to fit residues: 16.3786
Evaluate side-chains
  127 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 100
  time to evaluate  : 0.332 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   22 THR
Chi-restraints excluded: chain A residue   96 ILE
Chi-restraints excluded: chain A residue  108 ILE
Chi-restraints excluded: chain A residue  112 VAL
Chi-restraints excluded: chain A residue  132 MET
Chi-restraints excluded: chain A residue  147 THR
Chi-restraints excluded: chain A residue  174 VAL
Chi-restraints excluded: chain A residue  181 LEU
Chi-restraints excluded: chain A residue  210 LEU
Chi-restraints excluded: chain A residue  220 ASN
Chi-restraints excluded: chain A residue  236 LEU
Chi-restraints excluded: chain A residue  310 SER
Chi-restraints excluded: chain A residue  317 MET
Chi-restraints excluded: chain A residue  387 LEU
Chi-restraints excluded: chain B residue  110 LEU
Chi-restraints excluded: chain B residue  143 SER
Chi-restraints excluded: chain B residue  181 LEU
Chi-restraints excluded: chain B residue  199 THR
Chi-restraints excluded: chain B residue  236 LEU
Chi-restraints excluded: chain B residue  239 LEU
Chi-restraints excluded: chain B residue  387 LEU
Chi-restraints excluded: chain B residue  400 LEU
Chi-restraints excluded: chain B residue  417 ILE
Chi-restraints excluded: chain B residue  420 VAL
Chi-restraints excluded: chain B residue  448 ILE
Chi-restraints excluded: chain B residue  464 LEU
Chi-restraints excluded: chain B residue  470 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 51 optimal weight:    3.9990
   chunk 9 optimal weight:    2.9990
   chunk 37 optimal weight:    9.9990
   chunk 96 optimal weight:    5.9990
   chunk 111 optimal weight:    0.8980
   chunk 98 optimal weight:    9.9990
   chunk 6 optimal weight:    3.9990
   chunk 80 optimal weight:    2.9990
   chunk 15 optimal weight:    3.9990
   chunk 24 optimal weight:    0.2980
   chunk 94 optimal weight:    8.9990
   overall best weight:    2.2386

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
B 220 ASN
** B 560 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4611 r_free = 0.4611 target = 0.217567 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.3712 r_free = 0.3712 target = 0.132024 restraints weight = 11365.494|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3770 r_free = 0.3770 target = 0.136682 restraints weight = 5981.424|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3790 r_free = 0.3790 target = 0.138193 restraints weight = 4339.553|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3797 r_free = 0.3797 target = 0.139065 restraints weight = 3542.501|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3803 r_free = 0.3803 target = 0.139508 restraints weight = 3647.933|
|-----------------------------------------------------------------------------|
r_work (final): 0.3738
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7870
moved from start:          0.2303

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.049   9014  Z= 0.215
  Angle     :  0.721   9.742  12206  Z= 0.359
  Chirality :  0.043   0.175   1464
  Planarity :  0.004   0.063   1524
  Dihedral  :  7.212  57.218   1252
  Min Nonbonded Distance : 2.392

Molprobity Statistics.
  All-atom Clashscore : 11.12
  Ramachandran Plot:
    Outliers :  0.26 %
    Allowed  :  7.37 %
    Favored  : 92.37 %
  Rotamer:
    Outliers :  3.94 %
    Allowed  : 26.45 %
    Favored  : 69.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.89 (0.26), residues: 1140
  helix:  1.99 (0.19), residues: 752
  sheet: -0.00 (0.62), residues: 78
  loop : -2.98 (0.33), residues: 310

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 414 
 TYR   0.010   0.001   TYR A  83 
 PHE   0.017   0.002   PHE A 291 
 TRP   0.005   0.001   TRP A 104 
 HIS   0.010   0.001   HIS B 560 

Details of bonding type rmsd
  covalent geometry    : bond        0.00507 ( 9014)
  covalent geometry    : angle       0.72102 (12206)
  hydrogen bonds       : bond        0.04719 (  591)
  hydrogen bonds       : angle       4.34594 ( 1755)

*********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  2280 Ramachandran restraints generated.
    1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2280 Ramachandran restraints generated.
    1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  132 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 94
  time to evaluate  : 0.345 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  109 LYS cc_start: 0.8942 (mmtp) cc_final: 0.8468 (mmmt)
REVERT: A  212 GLU cc_start: 0.8337 (mp0) cc_final: 0.8030 (mp0)
REVERT: A  317 MET cc_start: 0.8688 (OUTLIER) cc_final: 0.7920 (mtt)
REVERT: A  525 MET cc_start: 0.2735 (ppp) cc_final: 0.1987 (ppp)
REVERT: B   94 LYS cc_start: 0.8113 (mmmm) cc_final: 0.7315 (ttmt)
REVERT: B  118 ASN cc_start: 0.8202 (t0) cc_final: 0.7907 (t0)
REVERT: B  181 LEU cc_start: 0.7768 (OUTLIER) cc_final: 0.7329 (mp)
REVERT: B  448 ILE cc_start: 0.5203 (OUTLIER) cc_final: 0.4931 (mt)
  outliers start: 38
  outliers final: 30
  residues processed: 127
  average time/residue: 0.0836
  time to fit residues: 15.5458
Evaluate side-chains
  126 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 93
  time to evaluate  : 0.363 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   22 THR
Chi-restraints excluded: chain A residue   96 ILE
Chi-restraints excluded: chain A residue  108 ILE
Chi-restraints excluded: chain A residue  112 VAL
Chi-restraints excluded: chain A residue  147 THR
Chi-restraints excluded: chain A residue  174 VAL
Chi-restraints excluded: chain A residue  181 LEU
Chi-restraints excluded: chain A residue  195 THR
Chi-restraints excluded: chain A residue  210 LEU
Chi-restraints excluded: chain A residue  220 ASN
Chi-restraints excluded: chain A residue  236 LEU
Chi-restraints excluded: chain A residue  279 THR
Chi-restraints excluded: chain A residue  310 SER
Chi-restraints excluded: chain A residue  317 MET
Chi-restraints excluded: chain A residue  387 LEU
Chi-restraints excluded: chain A residue  535 HIS
Chi-restraints excluded: chain B residue  110 LEU
Chi-restraints excluded: chain B residue  143 SER
Chi-restraints excluded: chain B residue  181 LEU
Chi-restraints excluded: chain B residue  195 THR
Chi-restraints excluded: chain B residue  199 THR
Chi-restraints excluded: chain B residue  220 ASN
Chi-restraints excluded: chain B residue  236 LEU
Chi-restraints excluded: chain B residue  239 LEU
Chi-restraints excluded: chain B residue  311 ILE
Chi-restraints excluded: chain B residue  341 ILE
Chi-restraints excluded: chain B residue  387 LEU
Chi-restraints excluded: chain B residue  417 ILE
Chi-restraints excluded: chain B residue  448 ILE
Chi-restraints excluded: chain B residue  464 LEU
Chi-restraints excluded: chain B residue  470 THR
Chi-restraints excluded: chain B residue  524 LEU
Chi-restraints excluded: chain B residue  540 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 13 optimal weight:    0.9990
   chunk 99 optimal weight:    0.7980
   chunk 16 optimal weight:    2.9990
   chunk 58 optimal weight:    0.3980
   chunk 75 optimal weight:    4.9990
   chunk 64 optimal weight:    0.9990
   chunk 70 optimal weight:    1.9990
   chunk 73 optimal weight:    0.5980
   chunk 86 optimal weight:    0.7980
   chunk 40 optimal weight:    0.0980
   chunk 72 optimal weight:    0.9980
   overall best weight:    0.5380

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
B 220 ASN
** B 560 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4589 r_free = 0.4589 target = 0.217942 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3883 r_free = 0.3883 target = 0.142676 restraints weight = 11382.939|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3824 r_free = 0.3824 target = 0.141587 restraints weight = 7735.194|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3807 r_free = 0.3807 target = 0.140955 restraints weight = 6282.344|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3825 r_free = 0.3825 target = 0.142289 restraints weight = 5322.847|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3825 r_free = 0.3825 target = 0.142400 restraints weight = 4414.848|
|-----------------------------------------------------------------------------|
r_work (final): 0.3788
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7628
moved from start:          0.2308

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   9014  Z= 0.129
  Angle     :  0.686  14.023  12206  Z= 0.338
  Chirality :  0.041   0.163   1464
  Planarity :  0.004   0.061   1524
  Dihedral  :  7.025  58.480   1252
  Min Nonbonded Distance : 2.403

Molprobity Statistics.
  All-atom Clashscore : 10.51
  Ramachandran Plot:
    Outliers :  0.26 %
    Allowed  :  6.75 %
    Favored  : 92.98 %
  Rotamer:
    Outliers :  3.01 %
    Allowed  : 27.39 %
    Favored  : 69.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.13 (0.26), residues: 1140
  helix:  2.17 (0.19), residues: 756
  sheet:  0.16 (0.63), residues: 78
  loop : -2.95 (0.33), residues: 306

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 414 
 TYR   0.017   0.001   TYR A 437 
 PHE   0.014   0.001   PHE A  57 
 TRP   0.004   0.001   TRP B 104 
 HIS   0.010   0.001   HIS B 560 

Details of bonding type rmsd
  covalent geometry    : bond        0.00271 ( 9014)
  covalent geometry    : angle       0.68604 (12206)
  hydrogen bonds       : bond        0.04229 (  591)
  hydrogen bonds       : angle       4.23320 ( 1755)

********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  2280 Ramachandran restraints generated.
    1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2280 Ramachandran restraints generated.
    1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  132 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 103
  time to evaluate  : 0.346 
Fit side-chains
   revert: symmetry clash
REVERT: A  109 LYS cc_start: 0.8898 (mmtp) cc_final: 0.8440 (mmmt)
REVERT: A  212 GLU cc_start: 0.8258 (mp0) cc_final: 0.8005 (mp0)
REVERT: B   94 LYS cc_start: 0.8059 (mmmm) cc_final: 0.7303 (ttmt)
REVERT: B  118 ASN cc_start: 0.8197 (t0) cc_final: 0.7882 (t0)
REVERT: B  181 LEU cc_start: 0.7686 (OUTLIER) cc_final: 0.7269 (mp)
REVERT: B  400 LEU cc_start: 0.7446 (OUTLIER) cc_final: 0.7184 (tp)
REVERT: B  448 ILE cc_start: 0.5518 (OUTLIER) cc_final: 0.5247 (mt)
  outliers start: 29
  outliers final: 25
  residues processed: 127
  average time/residue: 0.0763
  time to fit residues: 14.3848
Evaluate side-chains
  127 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 99
  time to evaluate  : 0.277 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   22 THR
Chi-restraints excluded: chain A residue   96 ILE
Chi-restraints excluded: chain A residue  108 ILE
Chi-restraints excluded: chain A residue  112 VAL
Chi-restraints excluded: chain A residue  132 MET
Chi-restraints excluded: chain A residue  147 THR
Chi-restraints excluded: chain A residue  181 LEU
Chi-restraints excluded: chain A residue  210 LEU
Chi-restraints excluded: chain A residue  220 ASN
Chi-restraints excluded: chain A residue  236 LEU
Chi-restraints excluded: chain A residue  310 SER
Chi-restraints excluded: chain A residue  317 MET
Chi-restraints excluded: chain A residue  387 LEU
Chi-restraints excluded: chain A residue  535 HIS
Chi-restraints excluded: chain B residue  143 SER
Chi-restraints excluded: chain B residue  181 LEU
Chi-restraints excluded: chain B residue  199 THR
Chi-restraints excluded: chain B residue  210 LEU
Chi-restraints excluded: chain B residue  239 LEU
Chi-restraints excluded: chain B residue  311 ILE
Chi-restraints excluded: chain B residue  341 ILE
Chi-restraints excluded: chain B residue  387 LEU
Chi-restraints excluded: chain B residue  400 LEU
Chi-restraints excluded: chain B residue  417 ILE
Chi-restraints excluded: chain B residue  448 ILE
Chi-restraints excluded: chain B residue  464 LEU
Chi-restraints excluded: chain B residue  470 THR
Chi-restraints excluded: chain B residue  524 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 41 optimal weight:    0.0370
   chunk 26 optimal weight:    5.9990
   chunk 3 optimal weight:    0.3980
   chunk 35 optimal weight:   30.0000
   chunk 59 optimal weight:    0.6980
   chunk 51 optimal weight:    8.9990
   chunk 48 optimal weight:   10.0000
   chunk 19 optimal weight:    2.9990
   chunk 95 optimal weight:    7.9990
   chunk 93 optimal weight:    0.0980
   chunk 20 optimal weight:    1.9990
   overall best weight:    0.6460

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
B 220 ASN
** B 560 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4591 r_free = 0.4591 target = 0.217779 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3870 r_free = 0.3870 target = 0.142046 restraints weight = 11270.841|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3806 r_free = 0.3806 target = 0.140107 restraints weight = 7067.969|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3794 r_free = 0.3794 target = 0.140020 restraints weight = 5431.830|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3813 r_free = 0.3813 target = 0.141380 restraints weight = 5184.428|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3813 r_free = 0.3813 target = 0.141416 restraints weight = 4253.036|
|-----------------------------------------------------------------------------|
r_work (final): 0.3766
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7665
moved from start:          0.2416

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   9014  Z= 0.130
  Angle     :  0.680  10.323  12206  Z= 0.335
  Chirality :  0.041   0.172   1464
  Planarity :  0.004   0.056   1524
  Dihedral  :  6.950  59.462   1252
  Min Nonbonded Distance : 2.418

Molprobity Statistics.
  All-atom Clashscore : 9.96
  Ramachandran Plot:
    Outliers :  0.26 %
    Allowed  :  7.02 %
    Favored  : 92.72 %
  Rotamer:
    Outliers :  3.42 %
    Allowed  : 27.28 %
    Favored  : 69.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.19 (0.26), residues: 1140
  helix:  2.23 (0.19), residues: 754
  sheet:  0.13 (0.63), residues: 78
  loop : -2.91 (0.33), residues: 308

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 414 
 TYR   0.010   0.001   TYR A 408 
 PHE   0.016   0.001   PHE A  57 
 TRP   0.004   0.001   TRP B 164 
 HIS   0.010   0.001   HIS B 560 

Details of bonding type rmsd
  covalent geometry    : bond        0.00280 ( 9014)
  covalent geometry    : angle       0.68046 (12206)
  hydrogen bonds       : bond        0.04138 (  591)
  hydrogen bonds       : angle       4.23896 ( 1755)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1650.02 seconds
wall clock time: 29 minutes 15.53 seconds (1755.53 seconds total)